RE: Documented evolution of new functions and behaviors in bacteria (Full Version)

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Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 10:05:16 AM)

quote:

This may sound a bit flippant but I mean it seriously. So what?

The thing is that you are focusing on how genetic change happens at the molecular level. But evolution is not a process that occurs at a molecular level.


Wait, wait. What do you mean evolution doesn’t occur at the molecular level? Obviously it begins at the molecular level, as a mutation is essentially a change in a molecule. And obviously the result is a molecular change (perhaps many); so implying it is irrelevant is extremely ignorant, particularly when the notion is essential.

Until you understand this basic notion of biology, the rest is rather moot.



gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 11:16:50 AM)

quote:

ORIGINAL: Jhud

quote:

This may sound a bit flippant but I mean it seriously. So what?

The thing is that you are focusing on how genetic change happens at the molecular level. But evolution is not a process that occurs at a molecular level.


Wait, wait. What do you mean evolution doesn’t occur at the molecular level? Obviously it begins at the molecular level, as a mutation is essentially a change in a molecule. And obviously the result is a molecular change (perhaps many); so implying it is irrelevant is extremely ignorant, particularly when the notion is essential.

Until you understand this basic notion of biology, the rest is rather moot.



Evolution is essentially a population level phenomenon. Species change is a matter of changes which initially occur in cells being dispersed through a population. That dispersal pattern is the meaning of evolution. That is why, in the neo-Darwinian concept, evolution is defined as changes in the proportional distribution of alleles in the gene pool. Note that it is not "changes in the alleles" but "changes in the distribution of alleles".

It is very important to grasp the fact that it is species that evolve. Individuals do not evolve. In complex life forms, an individual doesn't even change significantly when its cells mutate. Furthermore, the only mutations significant to evolution are those which occur in germ cells. A mutation in one of your sperm does not mean you, as an individual, have evolved. It only means that if a child is conceived from that particular sperm, it will have a DNA sequence it did not inherit from you or its mother.

Yes, genetic changes, mutations, are a prerequisite for evolution because some of them (not all by any means) generate differences in individuals--differences which may affect reproductive success. And it is certainly worthwhile to study the details of how such changes occur and of how they produce their effects.

But all this activity in a single cell is not evolution until we bring it to the species level. What is happening in the species is evolution, not what is happening in particular individual cells.

Evolution would be brought to a standstill without the molecular changes which introduce new possibilities. But that doesn't mean molecular change is evolution. In particular it doesn't mean that the modes and mechanisms of molecular change have any strong bearing on evolution.



Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 11:20:06 AM)

quote:

Evolution is essentially a population level phenomenon. Species change is a matter of changes which initially occur in cells being dispersed through a population. That dispersal pattern is the meaning of evolution. That is why, in the neo-Darwinian concept, evolution is defined as changes in the proportional distribution of alleles in the gene pool. Note that it is not "changes in the alleles" but "changes in the distribution of alleles".

It is very important to grasp the fact that it is species that evolve. Individuals do not evolve. In complex life forms, an individual doesn't even change significantly when its cells mutate. Furthermore, the only mutations significant to evolution are those which occur in germ cells. A mutation in one of your sperm does not mean you, as an individual, have evolved. It only means that if a child is conceived from that particular sperm, it will have a DNA sequence it did not inherit from you or its mother.

Yes, genetic changes, mutations, are a prerequisite for evolution because some of them (not all by any means) generate differences in individuals--differences which may affect reproductive success. And it is certainly worthwhile to study the details of how such changes occur and of how they produce their effects.

But all this activity in a single cell is not evolution until we bring it to the species level. What is happening in the species is evolution, not what is happening in particular individual cells.

Evolution would be brought to a standstill without the molecular changes which introduce new possibilities. But that doesn't mean molecular change is evolution. In particular it doesn't mean that the modes and mechanisms of molecular change have any strong bearing on evolution.


So, just to be clear, as you seem to have a tendency to not answer directly here - you agree with me that evolution begins with molecular change, and that the prodcut of evolution is essentially changes to the DNA molecule?



drmark -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 11:21:39 AM)

quote:

But that doesn't mean molecular change is evolution.
Oh, I'm slowly stirring - maybe we're on to something here. What does "evolution" actually mean to you, gluadys? Is universal common descent part of your definition of evolution?



gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 12:38:27 PM)

quote:

ORIGINAL: Jhud

So, just to be clear, as you seem to have a tendency to not answer directly here - you agree with me that evolution begins with molecular change, and that the prodcut of evolution is essentially changes to the DNA molecule?


Not quite. Molecular change is one initial prerequisite for the occurrence of evolution. The product of evolution is essentially changes in the species.

There are hundreds to trillions of DNA molecules even in one complex organism. A molecular change can only occur in one of them at a time. That is not evolution.

Evolution is the process of distributing a change from one cell in one organism to all cells in all (or most) organisms of the species.



gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 12:42:50 PM)

quote:

ORIGINAL: drmark

quote:

But that doesn't mean molecular change is evolution.
Oh, I'm slowly stirring - maybe we're on to something here. What does "evolution" actually mean to you, gluadys? Is universal common descent part of your definition of evolution?


See my reply to jhud.

Universal descent is a logical inferrence from the theory of evolution, but not a necessary conclusion. The acceptance of universal descent is based primarily on the supporting evidence and lack of falsification. What we know of the history of life on the planet concords well with the thesis of universal common descent.

Just to be sure of our terminology, are you conversant with the difference between universal common descent and single origin of life? The first does not necessarily imply the second.



Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 12:52:22 PM)

quote:

Not quite. Molecular change is one initial prerequisite for the occurrence of evolution. The product of evolution is essentially changes in the species.


Well, what constitutes a ‘change in the species’? Presumably this is a genetic difference, which is in essence a molecular difference, correct?

I mean this is pretty basic, you seem to be disagreeing just to be disagreeable..

quote:

There are hundreds to trillions of DNA molecules even in one complex organism. A molecular change can only occur in one of them at a time. That is not evolution.


Well, actually, it depends on the change we are discussing. A number of changes said to be examples of evolution are changes to a single nucleotide sequence.

quote:

Evolution is the process of distributing a change from one cell in one organism to all cells in all (or most) organisms of the species.


Actually, it would have to be a germline cell. And that change would still be molecular, and the resultant somatic cells propagated via selection would still be the product of that molecular change, or accumulation of molecular changes.



gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 1:43:03 PM)

quote:

ORIGINAL: Jhud
Well, what constitutes a ‘change in the species’? Presumably this is a genetic difference, which is in essence a molecular difference, correct?


A population of 95%+ white pepper moths becomes over the course of a century a population of 95% black pepper moths.

That is a change in the species.

Yes, the white and black moths are differentiated phenotypically by colour and genotypically by a genetic difference. But the genetic difference is not evolution. It is the changing proportion of the occurrence of the genetic difference that is evolution.


quote:


Well, actually, it depends on the change we are discussing. A number of changes said to be examples of evolution are changes to a single nucleotide sequence.


And as long as that change in a single nucleotide sits undistributed in a single cell or a single organism, there is no evolution. You have to move it from the place of first occurrence into the population at large. Only then does it become a change in the species.

The factor of distribution is why the mechanism of the genetic change is not particularly important. You seem to be saying that if the change is a modification in gene expression rather than a substitution of one codon for another in the gene itself, it is not evolution. But how a change happens or where it happens in the DNA sequence is less important than the ability of the change to propagate itself through the species.

To put it another way, a focus on the mechanisms of genetic change is a focus on what happens in single cells. And to that extent it is pre-evolution, not evolution. Evolution begins when that cell begins to propagate and distribute this change to other cells. And at that point, it doesn't really matter how the change took place. It only matters that there is an inheritable change being introduced to the population at large.

So if a change in gene expression causes that gene to propagate through the species in a way it did not before--that is just as much evolution as a change in the gene itself. It is still producing a changed species.

quote:

quote:

Evolution is the process of distributing a change from one cell in one organism to all cells in all (or most) organisms of the species.


Actually, it would have to be a germline cell.


Right. And it would have to be a germline cell which contributes to the production of a zygote.



Jhud -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 2:43:00 PM)

quote:

A population of 95%+ white pepper moths becomes over the course of a century a population of 95% black pepper moths.

That is a change in the species.

Yes, the white and black moths are differentiated phenotypically by colour and genotypically by a genetic difference. But the genetic difference is not evolution. It is the changing proportion of the occurrence of the genetic difference that is evolution.


You are simply avoiding the question. Obviously if there is a molecular change in one gene in a population of organisms, then there is a genetic difference in the population of organisms, is there not?

And when that change is propagated, then what is propagated is a molecular change, is it not?

So in essence, what we talk about in evolution, it is a change in the molecular structures present in organisms.

You do agree genes are molecular structures do you not?

quote:

And as long as that change in a single nucleotide sits undistributed in a single cell or a single organism, there is no evolution. You have to move it from the place of first occurrence into the population at large. Only then does it become a change in the species.


But evolution requires, and propagates a molecular change. And even a single molecular change represents a difference in the genetic information present in the population, does it not, as even one organism is a member of a population?

quote:

The factor of distribution is why the mechanism of the genetic change is not particularly important. You seem to be saying that if the change is a modification in gene expression rather than a substitution of one codon for another in the gene itself, it is not evolution. But how a change happens or where it happens in the DNA sequence is less important than the ability of the change to propagate itself through the species.


Well, no, it is very important.

If the genetic change is a product of complex of genes, the role of which is to effect various phenotypic changes in response to environmental changes, then that would be quite different than changing a gene so that it acts in a manner that it hadn’t previously.

So that if a cell didn’t previously excrete calcium, and a genetic change caused it to have this capability, then that would be quite different than a cell which had regulatory mechanisms that changed the amount of calcium excreted in response to environmental needs, would it not?

quote:

To put it another way, a focus on the mechanisms of genetic change is a focus on what happens in single cells. And to that extent it is pre-evolution, not evolution. Evolution begins when that cell begins to propagate and distribute this change to other cells. And at that point, it doesn't really matter how the change took place. It only matters that there is an inheritable change being introduced to the population at large.


I disagree; I think the inherent cellular mechanisms that regulate processes that normally occur in cells are significantly different than novel processes that would result from incidental genetic modification. It is, on the cellular level, the difference between pushing down the accelerator, and growing wings on ones car. Both produce change, but one is a product of the extant design, the other is novel to it. I think what is normally called ‘evolution’ is more likely the former than the latter.

quote:

So if a change in gene expression causes that gene to propagate through the species in a way it did not before--that is just as much evolution as a change in the gene itself. It is still producing a changed species.


Well yes; but that is like having cars produced with their accelerators set at different levels. It may be that the slower cars don’t make it over ditches and broken bridges, and so more fast cars are ultimately represented in the population, but this fails to explain how some cars become planes.



gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 3:25:21 PM)

quote:

ORIGINAL: Jhud
You are simply avoiding the question. Obviously if there is a molecular change in one organism in a population of organisms, then there is a genetic difference in the population of organisms, is there not?


Not one that changes the species. The individual is a variant, to be sure, but we need to see what happens to it. If that individual never reproduces, the species is unchanged.

quote:

And when that change is propagated, then what is propagated is a molecular change, is it not?

So in essence, what we talk about in evolution, it is a change in the molecular structures present in organisms.

You do agree genes are molecular structures do you not?


But evolution requires, and propagates a molecular change.


Yes, not quite, yes, and yes. In sentence two, to be picky, it is the propagation of the change that is evolution as stated in the fourth sentence.

quote:

And even a single molecular change represents a difference in the genetic information present in the population, does it not, as even one organism is a member of a population?


Only if the individual leaves surviving descendants. Otherwise the change is just a temporary blip, leaving the species unaffected.

quote:

If the genetic change is a product of complex of genes, the role of which is to effect various phenotypic changes in response to environmental changes, then that would be quite different than changing a gene so that it acts in a manner that it hadn’t previously.


I am not really seeing a difference here. How, in the first case, is the gene not acting differently from what it had previously?

quote:

So that if a cell didn’t previously excrete calcium, and a genetic change caused it to have this capability, then that would be quite different than a cell which had regulatory mechanisms that changed the amount of calcium excreted in response to environmental needs, would it not?


As far as the cell is concerned, yes. But genes are not cells. I am not certain that we are looking at a substantial difference in how the DNA is affected. Clearly, a cell must have the capacity to secrete calcium before the secretion is regulated. But does the introduction of that capacity require a different sort of genetic change than the change in regulation?


quote:

Well yes; but that is like having cars produced with their accelerators set at different levels. It may be that the slower cars don’t make it over ditches and broken bridges, and so more fast cars are ultimately represented in the population, but this fails to explain how some cars become planes.


Actually, it does. If we have managed to put wings on a car, we don't have a plane, yet. We have a car with wings that may glide to a soft landing in times of need. But it wouldn't take long to introduce changes to improve the gliding capacity and if purchasers began to demand cars with better gliding capacity not only for safety, but for the pleasure of enjoying the experience of flight, it wouldn't take long before vehicles specifically for flight were derived from the original car with wings.



drmark -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 3:31:44 PM)

quote:

What we know of the history of life on the planet concords well with the thesis of universal common descent
These bald-faced assertions of yours have now reached a level of absurdity. What we know of life's history fails to exceed even 6000 years of age. Unless you've made the archaeological find of the century, in which case I will nominate you for that Nobel Prize as well!



drj11 -> RE: Documented evolution of new functions and behaviors in bacteria (4/28/2008 6:19:57 PM)

quote:

ORIGINAL: drmark

quote:

What we know of the history of life on the planet concords well with the thesis of universal common descent
These bald-faced assertions of yours have now reached a level of absurdity. What we know of life's history fails to exceed even 6000 years of age. Unless you've made the archaeological find of the century, in which case I will nominate you for that Nobel Prize as well!


This is the funniest post I think I have read on this forum to date. Seriously, are you real?



drmark -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 8:29:22 AM)

quote:

This is the funniest post I think I have read on this forum to date. Seriously, are you real?
Please present evidence of human knowledge >6000 years old concerning the natural history of life on earth. I wait with bated breath, drj (drmark slowly turns blue while drj searches futilely for ancient written records).



drj11 -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 8:41:09 AM)

quote:

ORIGINAL: drmark

quote:

This is the funniest post I think I have read on this forum to date. Seriously, are you real?
Please present evidence of human knowledge >6000 years old concerning the natural history of life on earth. I wait with bated breath, drj (drmark slowly turns blue while drj searches futilely for ancient written records).


Dinosaurs. Case closed. That was easy.



DanJames -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 11:37:23 AM)

The fact that I am busy studying for finals and therefore not able to participate in this discussion is grieving me to no end. Anyway, I received the full text to the article that you guys wanted. If you want me to email it to you, please PM me with your email address. I haven't read it and won't have time to do so for a while.



Bettawrekonize -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 1:22:04 PM)

quote:

ORIGINAL: DanJames
The fact that I am busy studying for finals and therefore not able to participate in this discussion is grieving me to no end. Anyway, I received the full text to the article that you guys wanted. If you want me to email it to you, please PM me with your email address. I haven't read it and won't have time to do so for a while.


Yeah, I don't really have time to respond to this stuff right now either (but I would like to). If you are referring to the AIDS/HIV text, I would definitely like to read it when I do have time. I'll PM you my E - Mail address. I like things that pertain to immunology (and security in general; ie: how systems can be hacked, how to prevent a system from being hacked, etc...), I always find them interesting. I wish I had a book on immunology, does anyone have any recommendations (drmark)? Something new and up to date.



drmark -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 5:02:33 PM)

quote:

Dinosaurs. Case closed. That was easy.
So are dinosaurs now part of "we" (Homininae) or does some new discovery demonstrate their ability to reason? Try again, drj, and read your posts a little more rigorously this time!

I haven't even touched on the fact that you have no observational proof that dinos lived more than 6000 years ago. Ah, the holes evolutionists dig themselves into.



essentialsaltes -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 5:29:26 PM)

quote:

ORIGINAL: drmark

Please present evidence of human knowledge >6000 years old concerning the natural history of life on earth. I wait with bated breath,


How about this?



drmark -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 6:28:32 PM)

Yes, es, that's real evidence of human knowledge of certain animals existing in the past (barring overly fertile imaginations, interference by ETI, or some other such nonsense). However, there is no validated proof of the age of the cave paintings (note "estimated" to be 16K old) and more importantly, they do NOT show any observations of common descent, do they. Care to try again or are you ready to agree with me that "What we know of the history of life on the planet concords well with the thesis of universal common descent?" is a bald-faced assertion without any support whatsoever?



essentialsaltes -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 7:05:03 PM)

quote:

ORIGINAL: drmark

Yes, es, that's real evidence of human knowledge of certain animals existing in the past (barring overly fertile imaginations, interference by ETI, or some other such nonsense). However, there is no validated proof of the age of the cave paintings (note "estimated" to be 16K old)


Direct radiocarbon dating of the pigments in similar cave paintings yields ages of about 30,000 years (Chauvet cave).

quote:

and more importantly, they do NOT show any observations of common descent, do they.


It's quite clear that the aurochs and bison were both considered tasty, which suggested to the cavemen of yore that these species shared a common ancestor. A minority view among cavemen was that the two species were NOT closely related, but their coincidental tastiness was due to convergent evolution.

quote:

Care to try again or are you ready to agree with me that "What we know of the history of life on the planet concords well with the thesis of universal common descent?" is a bald-faced assertion without any support whatsoever?


It only has no support if you insist on denying that we can know anything about the world before human history began.



drmark -> RE: Documented evolution of new functions and behaviors in bacteria (4/29/2008 7:15:17 PM)

quote:

It only has no support if you insist on denying that we can know anything about the world before human history began.
You've been posting here for 6 months, es. Haven't you figured out by now that YEC scientists universally acknowledge that we can know LOTS OF THINGS about the world before human history began. We call that knowledge "Creator God's special revelation" (aka the Holy Bible) and its Truth is dramatically more reliable than human interpretations of evidence, untestable hypotheses, and wild conjectures taught in our public schools as irrefutable facts.



Agahnim -> RE: Documented evolution of new functions and behaviors in bacteria (4/30/2008 5:35:23 AM)

quote:

Yes, es, that's real evidence of human knowledge of certain animals existing in the past (barring overly fertile imaginations, interference by ETI, or some other such nonsense). However, there is no validated proof of the age of the cave paintings (note "estimated" to be 16K old) and more importantly, they do NOT show any observations of common descent, do they. Care to try again or are you ready to agree with me that "What we know of the history of life on the planet concords well with the thesis of universal common descent?" is a bald-faced assertion without any support whatsoever?

DrMark, I posted a thread on April 23rd describing a line of evidence for common descent between humans and chimps which can’t be explained any other way. It’s been on the front page of this forum for the past week. Here it is: http://forums.christianity.com/m_3346826/mpage_1/tm.htm

In that thread, I said that if anyone disagrees with the conclusion drawn by this essay, they should address the specific points made in it and explain where the flaws in them lie. Jhud has pointed out that this line of evidence does not point to any specific mechanism for evolution, but nobody (him included) has argued with the proposition that this is evidence for common descent. If you think the theory of common descent is “without any support whatsoever”, you apparently think there’s something wrong with the line of evidence presented in that essay. If that’s the case, why have you completely ignored that thread for the past week?



gluadys -> RE: Documented evolution of new functions and behaviors in bacteria (4/30/2008 7:33:18 AM)

quote:

ORIGINAL: drmark

Yes, es, that's real evidence of human knowledge of certain animals existing in the past (barring overly fertile imaginations, interference by ETI, or some other such nonsense). However, there is no validated proof of the age of the cave paintings (note "estimated" to be 16K old) and more importantly, they do NOT show any observations of common descent, do they. Care to try again or are you ready to agree with me that "What we know of the history of life on the planet concords well with the thesis of universal common descent?" is a bald-faced assertion without any support whatsoever?



So what is your thesis? That we cannot have knowledge of the history of life that was not available to ancient cave-painters? What tools (practical and conceptual) did they have to determine what a fossil is? to estimate the age of a rock stratum? to decipher the genetic basis of inheritance?

We know a good deal that they did not know and could not know.



essentialsaltes -> RE: Documented evolution of new functions and behaviors in bacteria (4/30/2008 10:15:38 AM)

quote:

ORIGINAL: drmark

quote:

It only has no support if you insist on denying that we can know anything about the world before human history began.
You've been posting here for 6 months, es. Haven't you figured out by now that YEC scientists universally acknowledge that we can know LOTS OF THINGS about the world before human history began. We call that knowledge "Creator God's special revelation" (aka the Holy Bible) and its Truth is dramatically more reliable than human interpretations of evidence, untestable hypotheses, and wild conjectures taught in our public schools as irrefutable facts.


Unfortunately for YEC, which only allows a few days of 'history' before the appearance of man, there are layers of fossil-bearing strata thousands of feet thick that contain no humans at all. This is not an interpretation. This is not untestable; it is tested by every palaeontologist in the field. It is an understatement to say that there are literally tons of evidence that the history of life on earth extends for eons before the emergence of humans.



drj11 -> RE: Documented evolution of new functions and behaviors in bacteria (4/30/2008 12:08:57 PM)

quote:

ORIGINAL: essentialsaltes

quote:

ORIGINAL: drmark

quote:

It only has no support if you insist on denying that we can know anything about the world before human history began.
You've been posting here for 6 months, es. Haven't you figured out by now that YEC scientists universally acknowledge that we can know LOTS OF THINGS about the world before human history began. We call that knowledge "Creator God's special revelation" (aka the Holy Bible) and its Truth is dramatically more reliable than human interpretations of evidence, untestable hypotheses, and wild conjectures taught in our public schools as irrefutable facts.


Unfortunately for YEC, which only allows a few days of 'history' before the appearance of man, there are layers of fossil-bearing strata thousands of feet thick that contain no humans at all. This is not an interpretation. This is not untestable; it is tested by every palaeontologist in the field. It is an understatement to say that there are literally tons of evidence that the history of life on earth extends for eons before the emergence of humans.


The sad part is, something like this shouldn't even have to be defended. Especially from a doctor.



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